Rm fix remaining bugs (#132)

* distmap: fix trim-args type
--trim-args should expect a string argument

* GenomeIndex.pm: remove checks for obsolete args
should also fix issue #127

* HadoopMapping.pm: mktemp needs template arg

* HadoopMapping.pm: exec to see mapper return code

bin/distmap

@@ -120,7 +120,7 @@ GetOptions(
 	"only-map"						=> \$only_map,
 	"only-hdfs-download"			=> \$only_hdfs_download,
 	"only-delete-temp"				=> \$only_delete_temp,
-	"trim-args"						=> \$trim_args,
+	"trim-args=s"						=> \$trim_args,
 	## other
 	"tmp-dir=s"						=> \$tmp_dir,
 	"output-format=s"				=> \$output_format,

lib/perl5/site_perl/GenomeIndex.pm

@@ -218,24 +218,6 @@ sub copy_exec {
 		$i++;
 	}
 
-
-	if (-e $args_dict->{"picard_mergesamfiles_jar"}) {
-		copy($args_dict->{"picard_mergesamfiles_jar"}, "$bin_dir_path/");
-	}
-
-	if (-e $args_dict->{"picard_sortsam_jar"}) {
-		copy($args_dict->{"picard_sortsam_jar"}, "$bin_dir_path/");
-	}
-
-	if (-e $args_dict->{"picard_jar"}) {
-		copy($args_dict->{"picard_jar"}, "$bin_dir_path/");
-	}
-
-
-	if (-e $args_dict->{"trim_script_path"}) {
-		copy($args_dict->{"trim_script_path"}, "$bin_dir_path/");
-	}
-
 	system("chmod -R +x $bin_dir_path/");
 
 

lib/perl5/site_perl/HadoopMapping.pm

@@ -459,11 +459,10 @@ sub write_hadoop_mapping_job {
 	print $ofh "job=\"$args_dict->{'job_desc'}"."_Mapping_"."$args_dict->{'read_folder'}\"\n\n";
 
   # now only works like this
-	print $ofh "mpsh=\$(mktemp)\n";
+	print $ofh "mpsh=\$(mktemp distmap.XXXXX)\n";
 	print $ofh "cat > \$mpsh << 'TOK'\n";
   print $ofh "#!/bin/bash\n";
-	print $ofh "./$args_dict->{'mapper_command'}\n";
-	print $ofh "wait\n";
+	print $ofh "exec ./$args_dict->{'mapper_command'}\n";
 	print $ofh "TOK\n";
 	print $ofh "chmod +x \$mpsh\n";